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Later that year, the Exeter was assigned to a mission patrolling the region surrounding the Omega system. While arranging preparations for a planetary survey of Omega IV, with the village elders, Tracey and his landing party contracted an unknown bacteriological disease. When the landing party, sans Tracey, transported back to the Exeter, they infected the entire crew. Tracey was able to survive due to remaining on the planet's surface where a natural immunization to the disease occurred due to the planet's atmosphere.

Six months later, after Starfleet lost contact with the Exeter, the USS Enterprise came across the missing ship. The Enterprise would discover the undamaged and apparently deserted Exeter in orbit of planet Omega IV; the ship's complement of four shuttlecraft was still present in the hangar deck. When boarded, the ship's helm was found left on automatic and the entire crew of four hundred were found dead, in the form of dehydrated crystals.

Upon reviewing the final log entry made by the ship's chief medical officer, Dr. Carter, it was discovered that the crew had died as a result of contamination from the, otherwise undetected, bacteriological disease. Captain Tracey would be located on the planet's surface, and eventually arrested for violating the Federation's Prime Directive.

With Tracey placed under arrest, and the mission over, Kirk declared the Exeter abandoned. (TOS: "The Omega Glory")

During filming on "The Omega Glory", a memo from Original Series producer Bob Justman to costume designer William Ware Theiss addressed the fact that the the Exeter crew wore their own, distinct assignment patch. Justman stated that this was an error, likely stemming from the insignia worn by the crew of the Antares in "Charlie X", which Justman stated was "the equivalent of merchant marine or freighter personnel". Justman stated that, going forward, all Starship personnel should wear the Starship emblem that the crew of the Enterprise wear. [2]

This episode was recreated by GAF as a three-disc stereoscopic View-Master presentation. A booklet recounting the story accompanied the discs, but it was not completely faithful to the shooting script. A "Lieutenant Raintree" is featured, and he was killed in the same manner as Lt. Galloway; "Phil Raintree" was a character in an early draft of this script, one being considered for filming as the second pilot.